Ingenuity Pathway Analysis training
Ingenuity Pathway Analysis allows searching and using information extracted from public databases and from full text article extraction. It categorizes its findings based on a in-house curated ontology, covering entities (proteins and other molecules), relationships between the entities (inhibites, activates,...) and functional information (pathways, biological process, disease,...).
The platform allows building biological networks on the fly, as well as computing enrichment from a user defined gene list. IPA is ideal to analyze microarray data, RNASeq results, masspec lists or any user-defined gene list and discover which biological features are over-represented that could be used to describe or interact with the biology behind the data.
The power of ingenuity lies within asking the right questions.
Contents
How to obtain IPA
IPA is a JAVA program that can be launched from their website. All you need is a webbrowser and JAVA runtime environment installed on your computer. To launch IPA, click 'LOGIN' at the top of the home page https://www.ingenuity.com and start IPA with the username and password obtain through BITS bits@vib.be (VIB members only!).
Exercises
- Ex 1 - Basic operations in IPA
- Ex 2 - Extracting useful information from IPA
- Ex 3 - Importing a gene or a gene-list into IPA
BITS IPA whitepapers
IPA recently retired the KEGG pathway from its platform, find here why KEGG has been removed from IPA and what HumanCyc is.
A useful cheat-sheet to decode IPA icons and abbreviations IPA quickcard (PDF)
Additional help
Additional resources can be found with IPA help menu items that will bring you to the IPA learning centre.
Online training topics
You will get a good idea of the power and richness of IPA by reading the list of IPA online Tutorials and Training reproduced below. Also check the youtube videos available from the IPA Training Resources page.
- Visually Relating to my Data: How do I visually relate this to my own data?
- Upload & Analyze Your Data Tutorial
- IPA Training Resources: A comprehensive list of training resources
- Upload and Analyze Example Data Tutorial
- Upstream Regulators Analysis Tutorial
- Downstream Effects Analysis Tutorial
- Analysis Results Tutorial
- Search for Genes Tutorial: Summary Statement: Covers a scenario of searching for all available info on the FASN gene and a specific search for FASN - AGT relationships.
- Human Isoforms View Tutorial
- Visualize Pathways Tutorial
- Upload & Analyze Your Data Tutorial
- IPA Training Resources: A comprehensive list of training resources
- Upload and Analyze Example Data Tutorial
- Upstream Regulators Analysis Tutorial
- Downstream Effects Analysis Tutorial
- Analysis Results Tutorial
- Search for Genes Tutorial: Summary Statement: Covers a scenario of searching for all available info on the FASN gene and a specific search for FASN - AGT relationships.
- Human Isoforms View Tutorial
- Visualize Pathways Tutorial
Archived BITS training sessions
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